A computer program for the analysis of dental models.

This paper presents the details and logic of a Fortran computer program which carries out routine clinical analysis of dental models resulting from impressions of the teeth and related structures, which are subsequently cast in plaster of Paris. The program is primarily intended for use by the orthodontist who is engaged in research or clinical practice, and is useful in studies related to changes in the dentition as a result of orthodontic treatment.     

Towards a biomolecular computer.

A new version of computing and information processing devices may result from major principles of information processing at molecular level. Non-discrete biomolecular computers based on these principles seems to be capable of solving problems of high computational complexity. One of the possible ways to implement these devices is based on biochemical non-linear dynamical systems. Means and ways to materialize biomolecular computers are discussed.     

A computer program for comparative analysis of nucleic acid sequences.

The programs offer the possibility of comparing pairs of homologous sequences in order to find out percentage of homology, number of identical and deviating nucleotides, of transitions and transversions and, derived from these, KNUC-values according to Kimura (1) and the corresponding standard error sigmaK. The sequences can be printed in pairs underneath each other, homologies are indicated by asterisks between the identical nucleotides. Out of a set of homologous sequences stored on a disk any number of sequences can be compared in pairs in this way, and a matrix containing either the percentage of homology values, the number of deviating nucleotides or the KNUC-values together with the corresponding standard errors can be sent to screen, printer or disk. A program will be available soon which creates a dendrogram representing the similarity between the sequences by use of an average linkage clustering method deduced from this matrix. The programs are written for Apple II computers using UCSD-PASCAL and for Sirius I/Victor 9000 computers using TURBO-PASCAL.     

A computer program for the morphometric analysis of cell profiles.

A computer program which yields values for the volumes, surface areas, and volume/surface area ratios of cell profiles is described for use on a desktop calculator (minicomputer). This program uses standard morphometric procedures, and incorporates data obtained from electron micrographs at two levels of sampling. The main program yields values for the 'average cell volume' at the tissue level of sampling. Two options at the cellular level of sampling are also included which yield values for the volumes, surface areas and volume/surface area ratios for the organelles. The first option allows an analysis of 'whole cells' containing equatorial profiles through the nucleus, while the second option permits a 'fractional' approach using segments of the cells. Finally, some of the advantages of the two options are discussed.     

A computer program package for relative survival analysis

A computer program package has been constructed for use in patient survival analyses for chronic diseases based on aggregated data. The central concept of the analyses--the relative survival rate--is the ratio of the observed survival rate of the patients to the survival rate expected in a group in the general population similar to the group of patients at the beginning of the follow-up (interval), with respect to age, sex and calendar time. This quantity is used to measure patient survival adjusted for the effect of mortality attributable to the competing risks of death without employing information on causes of death of individual patients. The package contains three alternative methods of estimating the relative survival rates, two different ways of estimating the expectation of life for the patients, and five methods of testing the relative survival patterns using information on the whole follow-up period. Conventional survival and competing risk analysis can also be performed with the package. It is hoped that the package will facilitate standardization of statistical methodology and terminology in long-term survival studies for chronic diseases.     

A computer program package for restriction map analysis and manipulation.

Programs for the calculation, storage and analysis of restriction maps derived from the analysis of partial digestion products from end labelled DNA (1,2,3) and their correlation with digestion - and hybridisation patterns in total digestions and Southern blot experiments are described. These programs allow direct input of gel patterns from partial or complete digestion experiments using a digitizer tablet, calculation of molecular weights and restriction maps, plotting of maps and actual or predicted fragment patterns and automated identification of overlapping cosmids from partial restriction mapping results. Programs are written in PASCAL and have been implemented on a VAX/VMS system, with a HP-7221T plotter and a digitizing tablet.     

A versatile digital computer program for non-linear regression analysis

1.

1. A general purpose digital computer program is described for application to biological experiments that require a non-linear regression analysis. The mathematical function, or model, to be fitted to a given set of experimental data is written as a section within the program. Given initial estimates for the parameters of the function, the program uses an iterative procedure to adjust the parameters until the sum of squares of residuals has converged to a minimum.     

A simple computer program with statistical tests for the analysis of enzyme kinetics.

A simple computer program that calculates the kinetic parameters of enzyme reactions is described. Parameters are determined by nonlinear, least-squares regression using either Marquardt-Levenberg or Gauss-Newton algorithms to find the minimum sum of squares. Three types of enzyme reactions can be analyzed: single substrate reactions (Michaelis-Menten and sigmoidal kinetics), enzyme activation at a fixed substrate value or enzyme inhibition at a fixed substrate value. The user can monitor goodness of fit through nonparametric statistical tests (performed automatically by the computer) and through visual examination of the pattern of residuals. The program is unique in providing equations for activator and inhibition analysis as well as in enabling the user to fix some of the parameters before regression analysis. The simplicity of the program makes it extremely useful for quickly determining kinetic parameters during the data-gathering process.     

A computer program for the calculation of amino acid analysis data

A program has been written for the computation of the data from amino acid analysis. This program will accept data both from integrators and from the hand calculation method. The program is written in a common language and is divided into two parts so as to convert the analytical data from the amino acid analyzer into several useful forms as desired. The first part calculates amino acid analysis of protein hydrolyzates and the second part calculates the composition of peptides.     

A computer program for long term anticoagulation control.

A computer program is described which calculates suggested daily anticoagulant dose schedules for long term patients. This program is a part of the real-time Information System for Thrombosis Centres. The program requires only the most recent information on the patient from the Information System's data base. This information consists of the latest two measured coagulation times, the previous dose schedule, the target and limiting values set by the physician to the coagulation time, and a very limited number of parameters accounting for the patient's anticoagulation history. A simple dose-response model is used to simulate and predict a coagulation time. By comparing this prediction with the measured coagulation time the program computes the necessary adjustment in the average dose and the appointment period. It gives remarks, if necessary. The Information System is used successfully for the majority of patients of Leiden Thrombosis Centre, where it operates as a part of a real-time Hospital Information System.     

A computer program to search for tRNA genes.

This paper describes a computer program that can find tRNA genes within long DNA sequences. The program obviates the need to map the tRNA genes.     

Computer simulated modeling of biomolecular systems.

This paper describes the algorithm of a program used to simulate three dimensional models of molecules. In addition to open ended molecules the program also enables simulation of structures with constraints in the form of cyclic regions or fixed location of particular atoms. Several molecules can be handled in a single run and each molecule can have any number of contraints. Further, any number of conformations can be obtained for each constrained region. The program can be used for research in several areas of molecular biology, e.g., structure determination, conformational analysis and topographic comparisons.     

A computer program for translating DNA sequences into protein.

This paper describes a comprehensive program for translating one or two DNA sequences into amino acid sequences. Written in FORTRAN, it was designed for maximum flexibility of use and easy maintenance, modification and portability. It has full comments throughout.     

A computer program for the analysis of dental arch form using the cubic spline function.

This paper presents the details and logic of a FORTRAN computer program which fits a cubic interpolatory spline to a set of data points digitized from an exact size photographic reproduction of a dental model. It also measures the length of the arc and computes a set of normals to the curve to be used in evaluating the error in the fit of the spline. The program is used in studies of dental arch form and is useful in evaluating changes in the form of the arches due to orthodontic treatment. The measurement of the arc length provides an adequate assessment of space available in the dental arch, which is of importance to the orthodontist.